@@ -1,5 +1,5 @@

-##' add tip point

+##' add tip point layer for a tree

 ##'

 ##'

 ##' @title geom_tippoint

@@ -7,6 +7,15 @@

 ##' @return tip point layer

 ##' @export

 ##' @author Guangchuang Yu

+##' @examples

+##' library(ggtree)

+##' tr<- rtree(15)

+##' x <- ggtree(tr)

+##' x + geom_tippoint()

+##' @references

+##' For more detailed demonstration, please refer to chapter 4.3.2 of 

+##' *Data Integration, Manipulation and Visualization of Phylogenetic Trees*

+##' <http://yulab-smu.top/treedata-book/index.html> by Guangchuang Yu.

 geom_tippoint <- function(mapping = NULL, data = NULL,

                        position = "identity", na.rm = FALSE,

                           show.legend = NA, inherit.aes = TRUE, ...) {

@@ -49,7 +58,7 @@ geom_tippoint <- function(mapping = NULL, data = NULL,

 ## }

-##' add node point

+##' add node point layer to a tree

 ##'

 ##'

 ##' @title geom_nodepoint

@@ -58,6 +67,14 @@ geom_tippoint <- function(mapping = NULL, data = NULL,

 ##' @importFrom ggplot2 aes_string

 ##' @export

 ##' @author Guangchuang Yu

+##' library(ggtree)

+##' tr<- rtree(15)

+##' x <- ggtree(tr)

+##' x + geom_nodepoint()

+##' @references

+##' For more detailed demonstration, please refer to chapter 4.3.2 of 

+##' *Data Integration, Manipulation and Visualization of Phylogenetic Trees*

+##' <http://yulab-smu.top/treedata-book/index.html> by Guangchuang Yu.

 geom_nodepoint <- function(mapping = NULL, data = NULL,

                        position = "identity", na.rm = FALSE,

                        show.legend = NA, inherit.aes = TRUE, ...) {

@@ -80,9 +97,9 @@ geom_nodepoint <- function(mapping = NULL, data = NULL,

 }

-##' geom_rootpoint is used to add root point

+##' geom_rootpoint is used to add root point layer to a tree

 ##'

-##' geom_rootpoint inherit from geom_point2, it is used to display and customize the points on the root

+##' geom_rootpoint inherit from geom_point2, and it is used to display and customize the points on the root

 ##'

 ##' @title geom_rootpoint

 ##' @inheritParams geom_point2

@@ -136,13 +153,13 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 #' If `inherit.aes = TRUE`, the mapping can be inherited from the plot mapping as

 #' specified in the call to `ggplot()`.

 #' @param data The data to be displayed in this layer. If 'NULL' (the default),

-#' the data is inherited from the plot data as specified in the call to 'ggplot()',

+#' the data is inherited from the plot data as specified in the call to `ggplot()`.

 #' @param stat Name of the statistical transformation to be used on the data for this layer.

 #' @param position Position adjustment.

-#' @param na.rm logical. If 'FALSE' (the default), missing values are removed with a warning. If 'TRUE', missing values are silently removed.

+#' @param na.rm logical. If 'FALSE' (default), missing values are removed with a warning. If 'TRUE', missing values are silently removed.

 #' @param show.legend logical. Should this layer be included in the legends?

 #' 'NA', the default, includes if any aesthetics are mapped. 'FALSE' never includes, and 'TRUE' always includes.

-#' @param inherit.aes logical (default is 'TRUE'). If 'FALSE', overrides the default aesthetics,

+#' @param inherit.aes logical (defaults to 'TRUE'). If 'FALSE', overrides the default aesthetics,

 #' rather then combining with them.

 #' @param ... addtional parameters that passed on to this layer. These are often aesthetics, used to set an aesthetic to a fixed value, like `colour = "red"` or `size = 3`.

 #' @importFrom ggplot2 layer

@@ -150,12 +167,12 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 #' \code{geom_point2()} understands the following aesthetics

 #'     \itemize{

 #'        \item \code{subset} logical expression indicating elements or rows to keep: missing values are taken as false; should be in aes().

-#'        \item \code{colour} the colour of point, default is black.

-#'        \item \code{fill} the colour of fill, default is black.

-#'        \item \code{alpha} the transparency of fill, default is 1.

-#'        \item \code{size} the size of point, default is 1.5.

-#'        \item \code{shape} specify a shape, default is 19.

-#'        \item \code{stroke} control point border thickness of point, default is 0.5.

+#'        \item \code{colour} the colour of point, defaults to "black".

+#'        \item \code{fill} the colour of fill, defaults to "black".

+#'        \item \code{alpha} the transparency of fill, defaults to 1.

+#'        \item \code{size} the size of point, defaults to 1.5.

+#'        \item \code{shape} specify a shape, defaults to 19.

+#'        \item \code{stroke} control point border thickness of point, defaults to 0.5.

 #'     }

 #' @seealso

 #'  [geom_point][ggplot2::geom_point]; 

@@ -89,19 +89,7 @@ geom_nodepoint <- function(mapping = NULL, data = NULL,

 ##' @return root point layer

 ##' @export

 ##' @author Guangchuang Yu

-##' @references 1. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam (2017). ggtree: an R package for

-##' visualization and annotation of phylogenetic trees with their covariates and

-##' other associated data. Methods in Ecology and Evolution, 8(1):28-36.

-##' <https://doi.org/10.1111/2041-210X.12628>

-##' 

-##' 2. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data 

-##' on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. <https://doi.org/10.1093/molbev/msy194>

-##' 

-##' 3. G Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in 

-##' Bioinformatics, 2020, 69:e96. <https://doi.org/10.1002/cpbi.96>

-##' 

-##' For more information about tree visualization, please refer to the online book

-##' <https://yulab-smu.top/treedata-book/>

+##' @references `r ggtree:::ggtree_references()`

 ##' @seealso

 ##'  [geom_point][ggplot2::geom_point]; 

 ##'  [geom_rootpoint] add point of root; 

@@ -80,14 +80,39 @@ geom_nodepoint <- function(mapping = NULL, data = NULL,

 }

-##' add root point

+##' geom_rootpoint is used to add root point

 ##'

+##' geom_rootpoint inherit from geom_point2, it is used to display and customize the points on the root

 ##'

 ##' @title geom_rootpoint

 ##' @inheritParams geom_point2

 ##' @return root point layer

 ##' @export

 ##' @author Guangchuang Yu

+##' @references 1. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam (2017). ggtree: an R package for

+##' visualization and annotation of phylogenetic trees with their covariates and

+##' other associated data. Methods in Ecology and Evolution, 8(1):28-36.

+##' <https://doi.org/10.1111/2041-210X.12628>

+##' 

+##' 2. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data 

+##' on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. <https://doi.org/10.1093/molbev/msy194>

+##' 

+##' 3. G Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in 

+##' Bioinformatics, 2020, 69:e96. <https://doi.org/10.1002/cpbi.96>

+##' 

+##' For more information about tree visualization, please refer to the online book

+##' <https://yulab-smu.top/treedata-book/>

+##' @seealso

+##'  [geom_point][ggplot2::geom_point]; 

+##'  [geom_rootpoint] add point of root; 

+##'  [geom_nodepoint] add points of internal nodes; 

+##'  [geom_tippoint] add points of external nodes (also known as tips or leaves).

+##' @examples

+##' library(ggtree)

+##' tr <- rtree(10)

+##' ##  add root point

+##' ggtree(tr) + geom_rootpoint()

+##' ggtree(tr) + geom_rootpoint(size=2,color="red",shape=2)

 geom_rootpoint <- function(mapping = NULL, data = NULL,

                            position = "identity", na.rm = FALSE,

                            show.legend = NA, inherit.aes = TRUE, ...) {

@@ -14,10 +14,16 @@ geom_tippoint <- function(mapping = NULL, data = NULL,

     if (is.null(mapping)) {

         mapping <- self_mapping

     } else {

-        if (!is.null(mapping$subset)) {

-            self_mapping <- aes_string(node = "node", subset = paste0(as.expression(get_aes_var(mapping, "subset")), '&isTip'))

+        if (is.null(mapping$subset)) {

+            mapping <- modifyList(self_mapping, mapping)   

+        } else { 

+            mapping <- modifyList(self_mapping, mapping)

+            subset_mapping <- aes_string(subset = paste0(

+                                             as.expression(get_aes_var(mapping, "subset")),

+                                             '&isTip')

+                                         )

+            mapping <- modifyList(mapping, subset_mapping)

         }

-        mapping <- modifyList(self_mapping, mapping)

     }

     geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, stat = StatTreeData, ...)

 }

@@ -59,10 +65,16 @@ geom_nodepoint <- function(mapping = NULL, data = NULL,

     if (is.null(mapping)) {

         mapping <- self_mapping

     } else {

-        if (!is.null(mapping$subset)) {

-            self_mapping <- aes_string(node = "node", subset = paste0(as.expression(get_aes_var(mapping, "subset")), '&!isTip'))

+        if (is.null(mapping$subset)) {

+            mapping <- modifyList(self_mapping, mapping)   

+        } else {

+            mapping <- modifyList(self_mapping, mapping)

+            subset_mapping <- aes_string(subset = paste0(

+                                             as.expression(get_aes_var(mapping, "subset")),

+                                             '&!isTip')

+                                         )

+            mapping <- modifyList(mapping, subset_mapping)               

         }

-        mapping %<>% modifyList(self_mapping)

     }

     geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, stat = StatTreeData, ...)

 }

@@ -84,7 +96,18 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

     if (is.null(mapping)) {

         mapping <- self_mapping

     } else {

-        mapping %<>% modifyList(self_mapping)

+        if (is.null(mapping$subset)) {

+            mapping <- modifyList(self_mapping, mapping)               

+        } else {

+            mapping <- modifyList(self_mapping, mapping)

+            subset_mapping <- aes_string(subset = paste0(

+                                             as.expression(get_aes_var(mapping, "subset")),

+                                             '&node==parent')

+                                         )

+            mapping <- modifyList(mapping, subset_mapping)   

+        }

+

+

     }

     geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, stat = StatTreeData, ...)

 }

@@ -90,20 +90,25 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 }

-#' geom_point2 support aes(subset) via setup_data

+#' geom_point2 is a modified version of geom_point that supports aes(subset)

+#'

+#' `geom_point2` creates scatterplots, just similar to `ggplot2::geom_point`. It extends the `ggplot2::geom_point` to support filtering via the `subset` aesthetic mapping (see Aesthetics section).

 #'

-#' `geom_point2` supports data.frame as input.And aesthetics of layer can be mapped.

-#' you can see the Aesthetics section to set parameters. 

 #'

 #' @title geom_point2

-#' @param mapping aes mapping

-#' @param data data

-#' @param stat Name of stat to modify data

-#' @param position position

-#' @param na.rm logical

-#' @param show.legend logical

-#' @param inherit.aes logical

-#' @param ... addktional parameter

+#' @param mapping Set of aesthetic mapping created by `aes()`.

+#' If `inherit.aes = TRUE`, the mapping can be inherited from the plot mapping as

+#' specified in the call to `ggplot()`.

+#' @param data The data to be displayed in this layer. If 'NULL' (the default),

+#' the data is inherited from the plot data as specified in the call to 'ggplot()',

+#' @param stat Name of the statistical transformation to be used on the data for this layer.

+#' @param position Position adjustment.

+#' @param na.rm logical. If 'FALSE' (the default), missing values are removed with a warning. If 'TRUE', missing values are silently removed.

+#' @param show.legend logical. Should this layer be included in the legends?

+#' 'NA', the default, includes if any aesthetics are mapped. 'FALSE' never includes, and 'TRUE' always includes.

+#' @param inherit.aes logical (default is 'TRUE'). If 'FALSE', overrides the default aesthetics,

+#' rather then combining with them.

+#' @param ... addtional parameters that passed on to this layer. These are often aesthetics, used to set an aesthetic to a fixed value, like `colour = "red"` or `size = 3`.

 #' @importFrom ggplot2 layer

 #' @section Aesthetics:

 #' \code{geom_point2()} understands the following aesthetics

@@ -119,8 +124,8 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 #' @seealso

 #'  [geom_point][ggplot2::geom_point]; 

 #'  [geom_rootpoint] add point of root; 

-#'  [geom_nodepoint] add point of node; 

-#'  [geom_tippoint] add point of tip.

+#'  [geom_nodepoint] add points of internal nodes; 

+#'  [geom_tippoint] add points of external nodes (also known as tips or leaves).

 #' @export

 #' @return point layer

 #' @author Guangchuang Yu 

@@ -130,24 +135,24 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 #' <https://doi.org/10.1111/2041-210X.12628>

 #' 

 #' 2. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data 

-#' on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194.

+#' on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. <https://doi.org/10.1093/molbev/msy194>

 #' 

 #' 3. G Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in 

-#' Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96.

+#' Bioinformatics, 2020, 69:e96. <https://doi.org/10.1002/cpbi.96>

 #' 

 #' For more information about tree visualization, please refer to the online book

-#' \url{https://yulab-smu.top/treedata-book/}

+#' <https://yulab-smu.top/treedata-book/>

 #' @export

 #' @examples

 #' library(ggtree)

 #' ## add point by aes(subset)

 #' tr <- rtree(10)

 #' # group tip and node

-#' ggtree(tr) + geom_point(aes(shape=isTip, color=isTip), size=3)

+#' ggtree(tr) + geom_point2(aes(shape=isTip, color=isTip), size=3)

 #' # specify a node to display

 #' ggtree(tr) + geom_point2(aes(subset=(node==15)), shape=21, size=5, fill='green')

 #' # specify a tip to display

-#' ggtree(tr) + geom_point2(aes(subset=(label=="t1")), shape=21, size=5, fill='green')

+#' ggtree(tr) + geom_point2(aes(subset=(label %in% c("t1", "t3"))), shape=21, size=5, fill='green')

 #' 

 #' ## color point with continuous variables

 #' library(ggtree)

@@ -157,7 +162,7 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 #' beast_tree <- read.beast(beast_file)

 #' p <- ggtree(beast_tree) +

 #'   geom_tiplab(hjust = -.1)+ 

-#'   geom_point(aes(fill = rate), shape = 21, size = 4) +

+#'   geom_nodepoint(aes(fill = rate), shape = 21, size = 4) +

 #'   scale_fill_continuous(low = 'blue', high = 'red') +

 #'   theme_tree2() + theme(legend.position = 'right')

 #' p

@@ -165,7 +170,7 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 geom_point2 <- function(mapping = NULL, data = NULL, stat = "identity",

                        position = "identity", na.rm = FALSE,

                        show.legend = NA, inherit.aes = TRUE, ...) {

-

+  

     default_aes <- aes_() # node=~node)

     if (is.null(mapping)) {

@@ -106,7 +106,7 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 #' @param ... addktional parameter

 #' @importFrom ggplot2 layer

 #' @section Aesthetics:

-#' \code{geom_point2()} understands the following aesthetics for rectangular layer

+#' \code{geom_point2()} understands the following aesthetics

 #'     \itemize{

 #'        \item \code{subset} logical expression indicating elements or rows to keep: missing values are taken as false; should be in aes().

 #'        \item \code{colour} the colour of point, default is black.

@@ -108,6 +108,7 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 #' @section Aesthetics:

 #' \code{geom_point2()} understands the following aesthetics for rectangular layer

 #'     \itemize{

+#'        \item \code{subset} logical expression indicating elements or rows to keep: missing values are taken as false; should be in aes().

 #'        \item \code{colour} the colour of point, default is black.

 #'        \item \code{fill} the colour of fill, default is black.

 #'        \item \code{alpha} the transparency of fill, default is 1.

@@ -133,6 +134,9 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 #' 

 #' 3. G Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in 

 #' Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96.

+#' 

+#' For more information about tree visualization, please refer to the online book

+#' \url{https://yulab-smu.top/treedata-book/}

 #' @export

 #' @examples

 #' library(ggtree)

@@ -158,8 +162,6 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 #'   theme_tree2() + theme(legend.position = 'right')

 #' p

 #' 

-#' ## For more information about tree visualization, please refer to our online book

-#' \url{https://yulab-smu.top/treedata-book/}

 geom_point2 <- function(mapping = NULL, data = NULL, stat = "identity",

                        position = "identity", na.rm = FALSE,

                        show.legend = NA, inherit.aes = TRUE, ...) {

@@ -90,24 +90,76 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 }

-##' geom_point2 support aes(subset) via setup_data

-##'

-##'

-##' @title geom_point2

-##' @param mapping aes mapping

-##' @param data data

-##' @param stat Name of stat to modify data

-##' @param position position

-##' @param na.rm logical

-##' @param show.legend logical

-##' @param inherit.aes logical

-##' @param ... addktional parameter

-##' @importFrom ggplot2 layer

-##' @export

-##' @seealso

-##' [geom_point][ggplot2::geom_point]

-##' @return point layer

-##' @author Guangchuang Yu

+#' geom_point2 support aes(subset) via setup_data

+#'

+#' `geom_point2` supports data.frame as input.And aesthetics of layer can be mapped.

+#' you can see the Aesthetics section to set parameters. 

+#'

+#' @title geom_point2

+#' @param mapping aes mapping

+#' @param data data

+#' @param stat Name of stat to modify data

+#' @param position position

+#' @param na.rm logical

+#' @param show.legend logical

+#' @param inherit.aes logical

+#' @param ... addktional parameter

+#' @importFrom ggplot2 layer

+#' @section Aesthetics:

+#' \code{geom_point2()} understands the following aesthetics for rectangular layer

+#'     \itemize{

+#'        \item \code{colour} the colour of point, default is black.

+#'        \item \code{fill} the colour of fill, default is black.

+#'        \item \code{alpha} the transparency of fill, default is 1.

+#'        \item \code{size} the size of point, default is 1.5.

+#'        \item \code{shape} specify a shape, default is 19.

+#'        \item \code{stroke} control point border thickness of point, default is 0.5.

+#'     }

+#' @seealso

+#'  [geom_point][ggplot2::geom_point]; 

+#'  [geom_rootpoint] add point of root; 

+#'  [geom_nodepoint] add point of node; 

+#'  [geom_tippoint] add point of tip.

+#' @export

+#' @return point layer

+#' @author Guangchuang Yu 

+#' @references 1. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam (2017). ggtree: an R package for

+#' visualization and annotation of phylogenetic trees with their covariates and

+#' other associated data. Methods in Ecology and Evolution, 8(1):28-36.

+#' <https://doi.org/10.1111/2041-210X.12628>

+#' 

+#' 2. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data 

+#' on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194.

+#' 

+#' 3. G Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in 

+#' Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96.

+#' @export

+#' @examples

+#' library(ggtree)

+#' ## add point by aes(subset)

+#' tr <- rtree(10)

+#' # group tip and node

+#' ggtree(tr) + geom_point(aes(shape=isTip, color=isTip), size=3)

+#' # specify a node to display

+#' ggtree(tr) + geom_point2(aes(subset=(node==15)), shape=21, size=5, fill='green')

+#' # specify a tip to display

+#' ggtree(tr) + geom_point2(aes(subset=(label=="t1")), shape=21, size=5, fill='green')

+#' 

+#' ## color point with continuous variables

+#' library(ggtree)

+#' library(treeio)

+#' library(ggplot2)

+#' beast_file <- system.file("examples/MCC_FluA_H3.tree", package="ggtree")

+#' beast_tree <- read.beast(beast_file)

+#' p <- ggtree(beast_tree) +

+#'   geom_tiplab(hjust = -.1)+ 

+#'   geom_point(aes(fill = rate), shape = 21, size = 4) +

+#'   scale_fill_continuous(low = 'blue', high = 'red') +

+#'   theme_tree2() + theme(legend.position = 'right')

+#' p

+#' 

+#' ## For more information about tree visualization, please refer to our online book

+#' \url{https://yulab-smu.top/treedata-book/}

 geom_point2 <- function(mapping = NULL, data = NULL, stat = "identity",

                        position = "identity", na.rm = FALSE,

                        show.legend = NA, inherit.aes = TRUE, ...) {

@@ -105,7 +105,7 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 ##' @importFrom ggplot2 layer

 ##' @export

 ##' @seealso

-##' \link[ggplot2]{geom_point}

+##' [geom_point][ggplot2::geom_point]

 ##' @return point layer

 ##' @author Guangchuang Yu

 geom_point2 <- function(mapping = NULL, data = NULL, stat = "identity",

@@ -15,7 +15,7 @@ geom_tippoint <- function(mapping = NULL, data = NULL,

         mapping <- self_mapping

     } else {

         if (!is.null(mapping$subset)) {

-            self_mapping <- aes_string(node = "node", subset = paste0(as.expression(mapping$subset), '&isTip'))

+            self_mapping <- aes_string(node = "node", subset = paste0(as.expression(get_aes_var(mapping, "subset")), '&isTip'))

         }

         mapping <- modifyList(self_mapping, mapping)

     }

@@ -60,7 +60,7 @@ geom_nodepoint <- function(mapping = NULL, data = NULL,

         mapping <- self_mapping

     } else {

         if (!is.null(mapping$subset)) {

-            self_mapping <- aes_string(node = "node", subset = paste0(as.expression(mapping$subset), '&!isTip'))

+            self_mapping <- aes_string(node = "node", subset = paste0(as.expression(get_aes_var(mapping, "subset")), '&!isTip'))

         }

         mapping %<>% modifyList(self_mapping)

     }

@@ -14,6 +14,9 @@ geom_tippoint <- function(mapping = NULL, data = NULL,

     if (is.null(mapping)) {

         mapping <- self_mapping

     } else {

+        if (!is.null(mapping$subset)) {

+            self_mapping <- aes_string(node = "node", subset = paste0(as.expression(mapping$subset), '&isTip'))

+        }

         mapping <- modifyList(self_mapping, mapping)

     }

     geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, stat = StatTreeData, ...)

@@ -46,16 +46,19 @@ geom_tippoint <- function(mapping = NULL, data = NULL,

 ##' @title geom_nodepoint

 ##' @inheritParams geom_point2

 ##' @return node point layer

+##' @importFrom ggplot2 aes_string

 ##' @export

 ##' @author Guangchuang Yu

 geom_nodepoint <- function(mapping = NULL, data = NULL,

                        position = "identity", na.rm = FALSE,

                        show.legend = NA, inherit.aes = TRUE, ...) {

-    node <- isTip <- NULL

-    self_mapping <- aes(node = node, subset = !isTip)

+    self_mapping <- aes_(node = ~node, subset = ~ (!isTip))

     if (is.null(mapping)) {

         mapping <- self_mapping

     } else {

+        if (!is.null(mapping$subset)) {

+            self_mapping <- aes_string(node = "node", subset = paste0(as.expression(mapping$subset), '&!isTip'))

+        }

         mapping %<>% modifyList(self_mapping)

     }

     geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, stat = StatTreeData, ...)

@@ -10,14 +10,13 @@

 geom_tippoint <- function(mapping = NULL, data = NULL,

                        position = "identity", na.rm = FALSE,

                           show.legend = NA, inherit.aes = TRUE, ...) {

-    isTip <- NULL

-    self_mapping <- aes(subset = isTip)

+    self_mapping <- aes_(node = ~node, subset = ~isTip)

     if (is.null(mapping)) {

         mapping <- self_mapping

     } else {

         mapping <- modifyList(self_mapping, mapping)

     }

-    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)

+    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, stat = StatTreeData, ...)

 }

 ## angle is not supported,

@@ -52,14 +51,14 @@ geom_tippoint <- function(mapping = NULL, data = NULL,

 geom_nodepoint <- function(mapping = NULL, data = NULL,

                        position = "identity", na.rm = FALSE,

                        show.legend = NA, inherit.aes = TRUE, ...) {

-    isTip <- NULL

-    self_mapping <- aes(subset = !isTip)

+    node <- isTip <- NULL

+    self_mapping <- aes(node = node, subset = !isTip)

     if (is.null(mapping)) {

         mapping <- self_mapping

     } else {

         mapping %<>% modifyList(self_mapping)

     }

-    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)

+    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, stat = StatTreeData, ...)

 }

@@ -75,13 +74,13 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

                            position = "identity", na.rm = FALSE,

                            show.legend = NA, inherit.aes = TRUE, ...) {

     isTip <- node <- parent <- NULL

-    self_mapping <- aes(subset = (node == parent))

+    self_mapping <- aes(node = node, subset = (node == parent))

     if (is.null(mapping)) {

         mapping <- self_mapping

     } else {

         mapping %<>% modifyList(self_mapping)

     }

-    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)

+    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, stat = StatTreeData, ...)

 }

@@ -91,6 +90,7 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 ##' @title geom_point2

 ##' @param mapping aes mapping

 ##' @param data data

+##' @param stat Name of stat to modify data

 ##' @param position position

 ##' @param na.rm logical

 ##' @param show.legend logical

@@ -102,12 +102,12 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 ##' \link[ggplot2]{geom_point}

 ##' @return point layer

 ##' @author Guangchuang Yu

-geom_point2 <- function(mapping = NULL, data = NULL,

+geom_point2 <- function(mapping = NULL, data = NULL, stat = "identity",

                        position = "identity", na.rm = FALSE,

                        show.legend = NA, inherit.aes = TRUE, ...) {

-    default_aes <- aes_(node=~node)

+    default_aes <- aes_() # node=~node)

     if (is.null(mapping)) {

         mapping <- default_aes

     } else {

@@ -117,7 +117,7 @@ geom_point2 <- function(mapping = NULL, data = NULL,

     layer(

         data = data,

         mapping = mapping,

-        stat = StatTreeData,

+        stat = stat,

         geom = GeomPointGGtree,

         position = position,

         show.legend = show.legend,

@@ -137,7 +137,7 @@ GeomPointGGtree <- ggproto("GeomPointGGtree", GeomPoint,

                            setup_data = function(data, params) {

                                if (is.null(data$subset))

                                    return(data)

-                               data[data$subset,]

+                               data[which(data$subset),]

                            }

                            ## ,

@@ -126,7 +126,7 @@ geom_point2 <- function(mapping = NULL, data = NULL,

             na.rm = na.rm,

             ...

         ),

-        if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE

+        check.aes = FALSE

     )

 }

@@ -126,7 +126,7 @@ geom_point2 <- function(mapping = NULL, data = NULL,

             na.rm = na.rm,

             ...

         ),

-        check.aes = FALSE

+        if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE

     )

 }

@@ -125,7 +125,8 @@ geom_point2 <- function(mapping = NULL, data = NULL,

         params = list(

             na.rm = na.rm,

             ...

-        )

+        ),

+        check.aes = FALSE

     )

 }

@@ -20,21 +20,25 @@ geom_tippoint <- function(mapping = NULL, data = NULL,

     geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)

 }

-geom_tippoint2 <- function(mapping=NULL, hjust=0, ...) {

-    angle <- NULL

-    isTip <- NULL

-    m1 <- aes(subset=(isTip & (angle < 90 | angle > 270)), angle=angle)

-    m2 <- aes(subset=(isTip & (angle >= 90 & angle <=270)), angle=angle+180)

-

-    if (!is.null(mapping)) {

-        m1 <- modifyList(mapping, m1)

-        m2 <- modifyList(mapping, m2)

-    }

-

-    list(geom_tippoint(m1, hjust=hjust, ...),

-         geom_tippoint(m2, hjust=1-hjust, ...)

-         )

-}

+## angle is not supported,

+## https://github.com/GuangchuangYu/ggtree/issues/77

+##

+##

+## geom_tippoint2 <- function(mapping=NULL, hjust=0, ...) {

+##     angle <- NULL

+##     isTip <- NULL

+##     m1 <- aes(subset=(isTip & (angle < 90 | angle > 270)), angle=angle)

+##     m2 <- aes(subset=(isTip & (angle >= 90 & angle <=270)), angle=angle+180)

+

+##     if (!is.null(mapping)) {

+##         m1 <- modifyList(mapping, m1)

+##         m2 <- modifyList(mapping, m2)

+##     }

+

+##     list(geom_tippoint(m1, hjust=hjust, ...),

+##          geom_tippoint(m2, hjust=1-hjust, ...)

+##          )

+## }

 ##' add node point

@@ -22,6 +22,7 @@ geom_tippoint <- function(mapping = NULL, data = NULL,

 geom_tippoint2 <- function(mapping=NULL, hjust=0, ...) {

     angle <- NULL

+    isTip <- NULL

     m1 <- aes(subset=(isTip & (angle < 90 | angle > 270)), angle=angle)

     m2 <- aes(subset=(isTip & (angle >= 90 & angle <=270)), angle=angle+180)

@@ -15,11 +15,27 @@ geom_tippoint <- function(mapping = NULL, data = NULL,

     if (is.null(mapping)) {

         mapping <- self_mapping

     } else {

-        mapping %<>% modifyList(self_mapping)

+        mapping <- modifyList(self_mapping, mapping)

     }

     geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)

 }

+geom_tippoint2 <- function(mapping=NULL, hjust=0, ...) {

+    angle <- NULL

+    m1 <- aes(subset=(isTip & (angle < 90 | angle > 270)), angle=angle)

+    m2 <- aes(subset=(isTip & (angle >= 90 & angle <=270)), angle=angle+180)

+

+    if (!is.null(mapping)) {

+        m1 <- modifyList(mapping, m1)

+        m2 <- modifyList(mapping, m2)

+    }

+

+    list(geom_tippoint(m1, hjust=hjust, ...),

+         geom_tippoint(m2, hjust=1-hjust, ...)

+         )

+}

+

+

 ##' add node point

 ##'

 ##'

@@ -1,13 +1,13 @@

 ##' add tip point

 ##'

-##' 

+##'

 ##' @title geom_tippoint

 ##' @inheritParams geom_point2

 ##' @return tip point layer

 ##' @export

 ##' @author Guangchuang Yu

-geom_tippoint <- function(mapping = NULL, data = NULL, 

+geom_tippoint <- function(mapping = NULL, data = NULL,

                        position = "identity", na.rm = FALSE,

                           show.legend = NA, inherit.aes = TRUE, ...) {

     isTip <- NULL

@@ -17,18 +17,18 @@ geom_tippoint <- function(mapping = NULL, data = NULL,

     } else {

         mapping %<>% modifyList(self_mapping)

     }

-    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)    

+    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)

 }

 ##' add node point

 ##'

-##' 

+##'

 ##' @title geom_nodepoint

 ##' @inheritParams geom_point2

 ##' @return node point layer

 ##' @export

 ##' @author Guangchuang Yu

-geom_nodepoint <- function(mapping = NULL, data = NULL, 

+geom_nodepoint <- function(mapping = NULL, data = NULL,

                        position = "identity", na.rm = FALSE,

                        show.legend = NA, inherit.aes = TRUE, ...) {

     isTip <- NULL

@@ -38,19 +38,19 @@ geom_nodepoint <- function(mapping = NULL, data = NULL,

     } else {

         mapping %<>% modifyList(self_mapping)

     }

-    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)    

+    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)

 }

 ##' add root point

 ##'

-##' 

+##'

 ##' @title geom_rootpoint

 ##' @inheritParams geom_point2

 ##' @return root point layer

 ##' @export

 ##' @author Guangchuang Yu

-geom_rootpoint <- function(mapping = NULL, data = NULL, 

+geom_rootpoint <- function(mapping = NULL, data = NULL,

                            position = "identity", na.rm = FALSE,

                            show.legend = NA, inherit.aes = TRUE, ...) {

     isTip <- node <- parent <- NULL

@@ -66,7 +66,7 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 ##' geom_point2 support aes(subset) via setup_data

 ##'

-##' 

+##'

 ##' @title geom_point2

 ##' @param mapping aes mapping

 ##' @param data data

@@ -85,14 +85,14 @@ geom_point2 <- function(mapping = NULL, data = NULL,

                        position = "identity", na.rm = FALSE,

                        show.legend = NA, inherit.aes = TRUE, ...) {

-    

+

     default_aes <- aes_(node=~node)

     if (is.null(mapping)) {

         mapping <- default_aes

     } else {

         mapping <- modifyList(mapping, default_aes)

     }

-    

+

     layer(

         data = data,

         mapping = mapping,

@@ -116,14 +116,16 @@ GeomPointGGtree <- ggproto("GeomPointGGtree", GeomPoint,

                                if (is.null(data$subset))

                                    return(data)

                                data[data$subset,]

-                           }  ## ,

-                           

+                           }

+

+                           ## ,

+

                            ## draw_panel = function(data, panel_scales, coord, na.rm = FALSE){

                            ##     GeomPoint$draw_panel(data, panel_scales, coord, na.rm)

                            ## },

-                           

+

                            ## draw_key = draw_key_point,

-                           

+

                            ## required_aes = c("x", "y"),

                            ## default_aes = aes(shape = 19, colour = "black", size = 1.5, fill = NA,

                            ##                   alpha = NA, stroke = 0.5)

@@ -7,7 +7,7 @@

 ##' @return tip point layer

 ##' @export

 ##' @author Guangchuang Yu

-geom_tippoint <- function(mapping = NULL, data = NULL, stat = "identity",

+geom_tippoint <- function(mapping = NULL, data = NULL, 

                        position = "identity", na.rm = FALSE,

                           show.legend = NA, inherit.aes = TRUE, ...) {

     isTip <- NULL

@@ -17,7 +17,7 @@ geom_tippoint <- function(mapping = NULL, data = NULL, stat = "identity",

     } else {

         mapping %<>% modifyList(self_mapping)

     }

-    geom_point2(mapping, data, stat, position, na.rm, show.legend, inherit.aes, ...)    

+    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)    

 }

 ##' add node point

@@ -28,7 +28,7 @@ geom_tippoint <- function(mapping = NULL, data = NULL, stat = "identity",

 ##' @return node point layer

 ##' @export

 ##' @author Guangchuang Yu

-geom_nodepoint <- function(mapping = NULL, data = NULL, stat = "identity",

+geom_nodepoint <- function(mapping = NULL, data = NULL, 

                        position = "identity", na.rm = FALSE,

                        show.legend = NA, inherit.aes = TRUE, ...) {

     isTip <- NULL

@@ -38,7 +38,7 @@ geom_nodepoint <- function(mapping = NULL, data = NULL, stat = "identity",

     } else {

         mapping %<>% modifyList(self_mapping)

     }

-    geom_point2(mapping, data, stat, position, na.rm, show.legend, inherit.aes, ...)    

+    geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)    

 }

@@ -50,7 +50,7 @@ geom_nodepoint <- function(mapping = NULL, data = NULL, stat = "identity",